Selecting animals for desired genotypic or potential phenotypic properties

Abstract

The invention relates to methods to select animals, such as mammals, in particular, domestic animals such as breeding animals or animals destined for slaughter, for having desired genotypic or potential phenotypic properties, in particular, related to muscle mass and/or fat deposition or, in the case of mammals, to teat number. The invention provides a method for selecting an animal for having desired genotypic or potential phenotypic properties comprising testing the animal, a parent of the animal or its progeny for the presence of a nucleic acid modification affecting the activity of an evolutionary conserved CpG island, located in intron 3 of an IGF2 gene and/or for the presence of a nucleic acid modification affecting binding of a nuclear factor to an IGF2 gene.

1 . A method for selecting an animal for having desired genotypic or potential phenotypic properties comprising testing said animal, a parent of said animal or its progeny for the presence of a nucleic acid modification affecting the activity of an evolutionary conserved CpG island, located in intron 3 of an IGF2 gene (SEQ ID NO: 1).  
     
     
         2 . A method for selecting an animal for having desired genotypic or potential phenotypic properties comprising testing said animal, a parent of said animal or its progeny for the presence of a nucleic acid modification affecting binding of a nuclear factor to an IGF2 gene.  
     
     
         3 . A method according to  claim 2  wherein said nuclear factor is capable of binding to a stretch of nucleotides which in the wild-type pig, mouse or human IGF2 gene is part of an evolutionary conserved CpG island, located in intron 3 of said IGF2 gene (SEQ ID NO:113, SEQ ID NO:114, SEQ ID NO:115 and SEQ ID NO:116).  
     
     
         4 . A method according to  claim 3  wherein said stretch is functionally equivalent to the sequence 5′-GATCCTTCGCCTAGGCTC(A/G)CAGCGCGGGAGCGA-3′(SEQ ID NO:1).  
     
     
         5 . A method according to  claim 1  wherein said nucleic acid modification comprises a nucleotide substitution.  
     
     
         6 . A method according to  claim 5  wherein said substitution in the pig comprises a G to A transition at IGF2-intron3-nt3072.  
     
     
         7 . A method according to  claim 2  wherein inhibiting binding of said nuclear factor to said IGF2 gene allows for modulating IGF2 mRNA transcription in a cell provided with said gene.  
     
     
         8 . A method according to  claim 1  wherein said desired genotypic or potential phenotypic properties comprise muscle mass, fat deposition or teat numbers.  
     
     
         9 . A method for modulating mRNA transcription of an IGF2 gene in a cell or organism provided with said gene comprising modulating the activity of an evolutionary conserved CpG island (SEQ ID NO:1), located in intron 3 of an IGF2 gene and/or modulating binding of a nuclear factor to an IGF2 gene.  
     
     
         10 . A method according to  claim 9  wherein said nuclear factor is capable of binding to a stretch of nucleotides which in the wild-type pig, mouse or human IGF2 gene is part of an evolutionary conserved CpG island, located in intron 3 of said IGF2 gene (SEQ ID NO:113, SEQ ID NO:114, SEQ ID NO:115 and SEQ ID NO:116).  
     
     
         11 . A method according to  claim 10  wherein said stretch is functionally equivalent to the sequence 5′-GATCCTTCGCCTAGGCTC(A/G)CAGCGCGGGAGCGA-3′(SEQ ID NO: 1).  
     
     
         12 . A method for identifying a compound capable of modulating mRNA transcription of an IGF2 gene in a cell or organism provided with said gene comprising: 
 providing a first cell or organism having a nucleic acid modification affecting the activity of an evolutionary conserved CpG island, located in intron 3 of an IGF2 gene and/or affecting binding of a nuclear factor to an IGF2 gene and a second cell or organism not having said modification;    further comprising providing said first or said second cell or organism with a test compound and determining IGF2 mRNA transcription in said first and second cell or organism.    
     
     
         13 . A method according to  claim 12  wherein said nuclear factor is capable of binding to a stretch of nucleotides which in the wild-type pig, mouse or human IGF2 gene is part of an evolutionary conserved CpG island, located in intron 3 of said IGF2 gene (SEQ ID NO: 113, SEQ ID NO: 114, SEQ ID NO: 115 and SEQ ID NO: 116).  
     
     
         14 . A method according to  claim 13  wherein said stretch is functionally equivalent to the sequence 5′-GATCCTTCGCCTAGGCTC(A/G)CAGCGCGGGAGCGA-3′(SEQ ID NO: 1).  
     
     
         15 . A method according to  claim 12  wherein said nucleic acid modification comprises a nucleotide substitution.  
     
     
         16 . A method according to  claim 15  wherein said substitution comprises a G to A transition which in the pig is located at IGF2-intron3-nt3072.  
     
     
         17 . A method for identifying a compound capable of modulating binding of a nuclear factor to an IFG2 gene: 
 comprising providing a stretch of nucleotides which in the wild-type pig, mouse or human IGF2 gene is part of an evolutionary conserved CpG island, located in intron 3 of said IGF2 gene;    further comprising providing a mixture of DNA-binding proteins derived from a nuclear extract of a cell;    further comprising providing a test compound; and    determining competition of binding of said mixture of DNA-binding proteins to said stretch of nucleotides in the presence or absence of said test compound.    
     
     
         18 . A method according to  claim 17  wherein said stretch is functionally equivalent to the sequence 5′-GATCCTTCGCCTAGGCTC(A/G)CAGCGCGGGAGCGA-3′(SEQ ID NO:1).  
     
     
         19 . A compound identifiable with a method according to  claim 13 .  
     
     
         20 . A compound according to  claim 19  comprising an oligonucleotide or analogue thereof functionally equivalent to the sequence 5′-GATCCTTCGCCTAGGCTC(A/G)CAGCGCGGGAGCGA-3′ (SEQ ID NO:1).  
     
     
         21 . A pharmaceutical composition comprising a compound according to  claim 19 .  
     
     
         22 . (canceled)  
     
     
         23 . (canceled)  
     
     
         24 . A method for modulating mRNA transcription of an IGF2 gene in a cell or organism provided with said gene comprising providing said cell or organism with a compound of  claim 19.